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<div class="section" id="module-atomeye">
<span id="atomeye-atomistic-configuration-viewer"></span><span id="atomeye"></span><h1>AtomEye atomistic configuration viewer<a class="headerlink" href="#module-atomeye" title="Permalink to this headline">¶</a></h1>
<p>This module provides the <a class="reference internal" href="#atomeye.AtomEyeViewer" title="atomeye.AtomEyeViewer"><code class="xref py py-class docutils literal notranslate"><span class="pre">AtomEyeViewer</span></code></a> class, which is a high-level
interface for interactive visualisation of Atoms objects using a <a class="reference external" href="http://www.jrkermode.co.uk/AtomEye">modified version</a> of the <a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A/">AtomEye</a>
atomistic configuration viewer.</p>
<p><a class="reference internal" href="atoms.html#quippy.atoms.Atoms" title="quippy.atoms.Atoms"><code class="xref py py-class docutils literal notranslate"><span class="pre">Atoms</span></code></a> and <a class="reference internal" href="io.html#quippy.io.AtomsList" title="quippy.io.AtomsList"><code class="xref py py-class docutils literal notranslate"><span class="pre">AtomsList</span></code></a>
objects can also be visualised with the <a class="reference internal" href="qlab.html#module-qlab" title="qlab: Interactive visualisation of atomic systems"><code class="xref py py-mod docutils literal notranslate"><span class="pre">qlab</span></code></a> module.</p>
<p>For example, to create and visualise and 8-atom silicon bulk cell:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">quippy.structures</span> <span class="k">import</span> <span class="n">diamond</span><span class="p">,</span> <span class="n">supercell</span>
<span class="kn">from</span> <span class="nn">atomeye</span> <span class="k">import</span> <span class="n">AtomEyeViewer</span>

<span class="n">d</span> <span class="o">=</span> <span class="n">diamond</span><span class="p">(</span><span class="mf">5.43</span><span class="p">,</span> <span class="mi">14</span><span class="p">)</span>
<span class="n">viewer</span> <span class="o">=</span> <span class="n">AtomEyeViewer</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>
</pre></div>
</div>
<p>A window will pop up containing the silicon unit cell, which you can manipulate
with the mouse, by issuing commands in the the python console or
with a variety of AtomEye <a class="reference external" href="http://li.mit.edu/Archive/Graphics/A3/A3.html#keybinding">keyboard shortcuts</a>. To save an image in PNG format:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">viewer</span><span class="o">.</span><span class="n">capture</span><span class="p">(</span><span class="s1">&#39;si8.png&#39;</span><span class="p">)</span>
</pre></div>
</div>
<img alt="si8.png" class="align-center" src="si8.png" />
<p>Then, to change the display to a <span class="math notranslate nohighlight">\(2       imes2   imes2\)</span> supercell of
bulk silicon, change the background colour to black, set the size and
save an image you’d do the following:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">at</span> <span class="o">=</span> <span class="n">supercell</span><span class="p">(</span><span class="n">d</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
<span class="n">viewer</span><span class="o">.</span><span class="n">show</span><span class="p">(</span><span class="n">at</span><span class="p">)</span>

<span class="n">viewer</span><span class="o">.</span><span class="n">change_bgcolor</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">))</span>
<span class="n">viewer</span><span class="o">.</span><span class="n">resize</span><span class="p">(</span><span class="mi">400</span><span class="p">,</span><span class="mi">300</span><span class="p">)</span>
<span class="n">viewer</span><span class="o">.</span><span class="n">capture</span><span class="p">(</span><span class="s1">&#39;si2x2x2.png&#39;</span><span class="p">)</span>
</pre></div>
</div>
<img alt="_images/si2x2x2.png" class="align-center" src="_images/si2x2x2.png" />
<p>Module attributes:</p>
<dl class="attribute">
<dt id="atomeye.viewers">
<code class="descclassname">atomeye.</code><code class="descname">viewers</code><a class="headerlink" href="#atomeye.viewers" title="Permalink to this definition">¶</a></dt>
<dd><p>Dictionary mapping <cite>window_id</cite> to <code class="xref py py-class docutils literal notranslate"><span class="pre">AtomEyeView</span></code> instances. There
is one entry for each currently open AtomEye view window.</p>
</dd></dl>

<dl class="attribute">
<dt id="atomeye.default_state">
<code class="descclassname">atomeye.</code><code class="descname">default_state</code><a class="headerlink" href="#atomeye.default_state" title="Permalink to this definition">¶</a></dt>
<dd><p>Dictionary of key/value pairs passed to <code class="xref py py-meth docutils literal notranslate"><span class="pre">AtomEyeView.update()</span></code> when
a new window is created. Change this dictionary to modfiy the properties
of new windows. The initial value is as follows:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">default_state</span> <span class="o">=</span> <span class="p">{</span>
    <span class="s1">&#39;variables&#39;</span> <span class="p">:</span> <span class="p">{</span><span class="s1">&#39;n-&gt;xtal_mode&#39;</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
                   <span class="s1">&#39;n-&gt;suppress_printout&#39;</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
                   <span class="s1">&#39;n-&gt;bond_mode&#39;</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
                   <span class="s1">&#39;n-&gt;atom_r_ratio&#39;</span><span class="p">:</span> <span class="mf">0.5</span><span class="p">,</span>
                   <span class="s1">&#39;n-&gt;small_cell_err_handler&#39;</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span>
                   <span class="s1">&#39;key-&gt;BackSpace&#39;</span><span class="p">:</span> <span class="s1">&#39;load_config_backward&#39;</span>
                   <span class="p">},</span>
    <span class="s1">&#39;commands&#39;</span><span class="p">:</span> <span class="p">[</span><span class="s1">&#39;xtal_origin_goto 0.5 0.5 0.5&#39;</span><span class="p">,</span>
                 <span class="s1">&#39;toggle_parallel_projection&#39;</span><span class="p">],</span>
    <span class="s1">&#39;cutoff_lengths&#39;</span><span class="p">:</span> <span class="p">[]</span>
<span class="p">}</span>
</pre></div>
</div>
</dd></dl>

<p>Module contents for <a class="reference internal" href="#module-atomeye" title="atomeye: AtomEye atomistic configuration viewer"><code class="xref py py-mod docutils literal notranslate"><span class="pre">atomeye</span></code></a>:</p>
<p class="rubric">Classes</p>
<table border="1" class="longtable docutils">
<colgroup>
<col width="10%" />
<col width="90%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer" title="atomeye.AtomEyeViewer"><code class="xref py py-obj docutils literal notranslate"><span class="pre">AtomEyeViewer</span></code></a>([atoms,&nbsp;viewer_id,&nbsp;copy,&nbsp;…])</td>
<td>View an atomic configuration or trajectory with AtomEye</td>
</tr>
</tbody>
</table>
<p class="rubric">Functions</p>
<table border="1" class="longtable docutils">
<colgroup>
<col width="10%" />
<col width="90%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.view" title="atomeye.view"><code class="xref py py-obj docutils literal notranslate"><span class="pre">view</span></code></a>(atoms,&nbsp;**kwargs)</td>
<td>Convenience wrapper to create/reuse a default <cite>AtomEyeViewer</cite></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.redraw" title="atomeye.redraw"><code class="xref py py-obj docutils literal notranslate"><span class="pre">redraw</span></code></a>()</td>
<td>Redraw current AtomEye window, keeping Atoms and settings the same.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.run_command" title="atomeye.run_command"><code class="xref py py-obj docutils literal notranslate"><span class="pre">run_command</span></code></a>(command)</td>
<td>Run a command in current AtomEye thread.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.run_script" title="atomeye.run_script"><code class="xref py py-obj docutils literal notranslate"><span class="pre">run_script</span></code></a>(script)</td>
<td>Run commands from the file script, in a blocking fashion.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.close" title="atomeye.close"><code class="xref py py-obj docutils literal notranslate"><span class="pre">close</span></code></a>()</td>
<td>Close the current viewer window.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.setp" title="atomeye.setp"><code class="xref py py-obj docutils literal notranslate"><span class="pre">setp</span></code></a>(self,&nbsp;key,&nbsp;value)</td>
<td>Run the AtomEye command “set key value”</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.save_script" title="atomeye.save_script"><code class="xref py py-obj docutils literal notranslate"><span class="pre">save_script</span></code></a>(filename)</td>
<td>Save AtomEye viewer settings to a file.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.toggle_coordination_coloring" title="atomeye.toggle_coordination_coloring"><code class="xref py py-obj docutils literal notranslate"><span class="pre">toggle_coordination_coloring</span></code></a>()</td>
<td>Turn on or off colouring by coordination number (key “k”)</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.translate" title="atomeye.translate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate</span></code></a>(axis,&nbsp;delta)</td>
<td>Translate system along <cite>axis</cite> by an amount <cite>delta</cite> (key “Ctrl+left/right/up/down”)</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.shift_xtal" title="atomeye.shift_xtal"><code class="xref py py-obj docutils literal notranslate"><span class="pre">shift_xtal</span></code></a>(axis,&nbsp;delta)</td>
<td>Shift crystal within periodic boundaries along <cite>axis</cite> by <cite>delta</cite> (key “Shift+left/right/up/down”).</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.rotate" title="atomeye.rotate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">rotate</span></code></a>(axis,&nbsp;theta)</td>
<td>Rotate around <cite>axis</cite> by angle <cite>theta</cite>.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.advance" title="atomeye.advance"><code class="xref py py-obj docutils literal notranslate"><span class="pre">advance</span></code></a>(delta)</td>
<td>Move the camera forward by <cite>delta</cite>.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.shift_cutting_plane" title="atomeye.shift_cutting_plane"><code class="xref py py-obj docutils literal notranslate"><span class="pre">shift_cutting_plane</span></code></a>(delta)</td>
<td>Shift the current cutting plane by an amount <cite>delta</cite>.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.change_bgcolor" title="atomeye.change_bgcolor"><code class="xref py py-obj docutils literal notranslate"><span class="pre">change_bgcolor</span></code></a>(color)</td>
<td>Change the viewer background colour to <cite>color</cite>, which should be a RGB tuple with three floats in range 0..1.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.change_atom_r_ratio" title="atomeye.change_atom_r_ratio"><code class="xref py py-obj docutils literal notranslate"><span class="pre">change_atom_r_ratio</span></code></a>(delta)</td>
<td>Change the size of the balls used to draw the atoms by <cite>delta</cite>.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.change_bond_radius" title="atomeye.change_bond_radius"><code class="xref py py-obj docutils literal notranslate"><span class="pre">change_bond_radius</span></code></a>(delta)</td>
<td>Change the radius of the cylinders used the draw bonds by <cite>delta</cite>.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.change_view_angle_amplification" title="atomeye.change_view_angle_amplification"><code class="xref py py-obj docutils literal notranslate"><span class="pre">change_view_angle_amplification</span></code></a>(delta)</td>
<td>Change the amplification of the view angle by <cite>delta</cite>.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.toggle_parallel_projection" title="atomeye.toggle_parallel_projection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">toggle_parallel_projection</span></code></a>()</td>
<td>Toggle between parallel and perspective projections.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.toggle_bond_mode" title="atomeye.toggle_bond_mode"><code class="xref py py-obj docutils literal notranslate"><span class="pre">toggle_bond_mode</span></code></a>()</td>
<td>Turn on or off bonds.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.toggle_small_cell_mode" title="atomeye.toggle_small_cell_mode"><code class="xref py py-obj docutils literal notranslate"><span class="pre">toggle_small_cell_mode</span></code></a>()</td>
<td>Toggle between two different behaviours for when cell is smaller than r_cut/2:</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.normal_coloring" title="atomeye.normal_coloring"><code class="xref py py-obj docutils literal notranslate"><span class="pre">normal_coloring</span></code></a>()</td>
<td>Return to normal colouring of the atoms (key “o”).</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.aux_property_coloring" title="atomeye.aux_property_coloring"><code class="xref py py-obj docutils literal notranslate"><span class="pre">aux_property_coloring</span></code></a>(auxprop)</td>
<td>Colour the currently viewed atoms according to <cite>auxprop</cite>.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.central_symmetry_coloring" title="atomeye.central_symmetry_coloring"><code class="xref py py-obj docutils literal notranslate"><span class="pre">central_symmetry_coloring</span></code></a>()</td>
<td>Colour atoms by centro-symmetry parameter.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.change_aux_property_threshold" title="atomeye.change_aux_property_threshold"><code class="xref py py-obj docutils literal notranslate"><span class="pre">change_aux_property_threshold</span></code></a>(lower,&nbsp;upper)</td>
<td>Change the lower and upper aux property thresholds.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.reset_aux_property_thresholds" title="atomeye.reset_aux_property_thresholds"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reset_aux_property_thresholds</span></code></a>()</td>
<td>Reset aux property thresholds to automatic values.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.toggle_aux_property_thresholds_saturation" title="atomeye.toggle_aux_property_thresholds_saturation"><code class="xref py py-obj docutils literal notranslate"><span class="pre">toggle_aux_property_thresholds_saturation</span></code></a>()</td>
<td>Toggle between saturated colouring and invisibility for values outside aux prop thresholds.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.toggle_aux_property_thresholds_rigid" title="atomeye.toggle_aux_property_thresholds_rigid"><code class="xref py py-obj docutils literal notranslate"><span class="pre">toggle_aux_property_thresholds_rigid</span></code></a>()</td>
<td>Toggle between floating and rigid aux property thresholds when moving between frames</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.rcut_patch" title="atomeye.rcut_patch"><code class="xref py py-obj docutils literal notranslate"><span class="pre">rcut_patch</span></code></a>(sym1,&nbsp;sym2,&nbsp;value[,&nbsp;absolute])</td>
<td>Change the cutoff distance for <cite>sym1</cite>–<cite>sym2</cite> bonds by <cite>delta</cite>.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.select_gear" title="atomeye.select_gear"><code class="xref py py-obj docutils literal notranslate"><span class="pre">select_gear</span></code></a>(gear)</td>
<td>Change the AtomEye gear to <cite>gear</cite></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.cutting_plane" title="atomeye.cutting_plane"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cutting_plane</span></code></a>(n,&nbsp;d,&nbsp;s)</td>
<td>Create a new cutting plane with index <cite>n</cite>, normal <cite>d</cite>, and fractional displacement <cite>s</cite>.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.shift_cutting_plane_to_anchor" title="atomeye.shift_cutting_plane_to_anchor"><code class="xref py py-obj docutils literal notranslate"><span class="pre">shift_cutting_plane_to_anchor</span></code></a>(n)</td>
<td>Move the cutting plane with index <cite>n</cite> to the anchor</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.delete_cutting_plane" title="atomeye.delete_cutting_plane"><code class="xref py py-obj docutils literal notranslate"><span class="pre">delete_cutting_plane</span></code></a>(n)</td>
<td>Delete the cutting plane with index <cite>n</cite></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.flip_cutting_plane" title="atomeye.flip_cutting_plane"><code class="xref py py-obj docutils literal notranslate"><span class="pre">flip_cutting_plane</span></code></a>(n)</td>
<td>Flip the cutting plane with index <cite>n</cite></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.capture" title="atomeye.capture"><code class="xref py py-obj docutils literal notranslate"><span class="pre">capture</span></code></a>(filename[,&nbsp;resolution])</td>
<td>Render the current view to image <cite>filename</cite></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.change_wireframe_mode" title="atomeye.change_wireframe_mode"><code class="xref py py-obj docutils literal notranslate"><span class="pre">change_wireframe_mode</span></code></a>()</td>
<td>Change the display mode for the unit cell box.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.change_cutting_plane_wireframe_mode" title="atomeye.change_cutting_plane_wireframe_mode"><code class="xref py py-obj docutils literal notranslate"><span class="pre">change_cutting_plane_wireframe_mode</span></code></a>()</td>
<td>Change the display mode for cutting planes</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.get_frame" title="atomeye.get_frame"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_frame</span></code></a>()</td>
<td>Get index of frame currently being viewed</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.set_frame" title="atomeye.set_frame"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_frame</span></code></a>(frame)</td>
<td>Set current frame index to <cite>frame</cite></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.get_delta" title="atomeye.get_delta"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_delta</span></code></a>()</td>
<td>Get frame increment rate</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.set_delta" title="atomeye.set_delta"><code class="xref py py-obj docutils literal notranslate"><span class="pre">set_delta</span></code></a>(delta)</td>
<td>Set frame increment rate</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.first" title="atomeye.first"><code class="xref py py-obj docutils literal notranslate"><span class="pre">first</span></code></a>()</td>
<td>Show the first frame (frame 0).</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.last" title="atomeye.last"><code class="xref py py-obj docutils literal notranslate"><span class="pre">last</span></code></a>()</td>
<td>Show the last frame, i.e.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.forward" title="atomeye.forward"><code class="xref py py-obj docutils literal notranslate"><span class="pre">forward</span></code></a>([delta])</td>
<td>Move forward by <cite>delta</cite> frames (default value is gcv().delta).</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.backward" title="atomeye.backward"><code class="xref py py-obj docutils literal notranslate"><span class="pre">backward</span></code></a>([delta])</td>
<td>Move backward by <cite>delta</cite> frames (default values is gcv().delta).</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.load_atom_color" title="atomeye.load_atom_color"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_atom_color</span></code></a>(filename)</td>
<td>Load atom colours from a .clr file.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.load_aux" title="atomeye.load_aux"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_aux</span></code></a>(filename)</td>
<td>Load aux property values from a .aux file.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.look_at_the_anchor" title="atomeye.look_at_the_anchor"><code class="xref py py-obj docutils literal notranslate"><span class="pre">look_at_the_anchor</span></code></a>()</td>
<td>Equivalent to pressing the <cite>a</cite> key</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.observer_goto" title="atomeye.observer_goto"><code class="xref py py-obj docutils literal notranslate"><span class="pre">observer_goto</span></code></a>()</td>
<td>Prompt for fractional position and move the observer there</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.xtal_origin_goto" title="atomeye.xtal_origin_goto"><code class="xref py py-obj docutils literal notranslate"><span class="pre">xtal_origin_goto</span></code></a>(s)</td>
<td>Move the crystal origin to fractional coordinates <cite>s</cite></td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.find_atom" title="atomeye.find_atom"><code class="xref py py-obj docutils literal notranslate"><span class="pre">find_atom</span></code></a>(i)</td>
<td>Set the anchor to the atom with index <cite>i</cite>.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.resize" title="atomeye.resize"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resize</span></code></a>(width,&nbsp;height)</td>
<td>Resize the current window to <cite>width</cite> x <cite>height</cite> pixels.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.change_aux_colormap" title="atomeye.change_aux_colormap"><code class="xref py py-obj docutils literal notranslate"><span class="pre">change_aux_colormap</span></code></a>(n)</td>
<td>Select the <cite>n</cite>-th auxiliary property colourmap.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.draw_arrows" title="atomeye.draw_arrows"><code class="xref py py-obj docutils literal notranslate"><span class="pre">draw_arrows</span></code></a>(property[,&nbsp;scale_factor,&nbsp;…])</td>
<td>Draw arrows on each atom, based on a vector property</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.wait" title="atomeye.wait"><code class="xref py py-obj docutils literal notranslate"><span class="pre">wait</span></code></a>()</td>
<td>Sleep until current AtomEye viewer has finished processing all queued events.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.display" title="atomeye.display"><code class="xref py py-obj docutils literal notranslate"><span class="pre">display</span></code></a>()</td>
<td>Display snapshot from current viewer in Jupyter notebook</td>
</tr>
</tbody>
</table>
<dl class="class">
<dt id="atomeye.AtomEyeViewer">
<em class="property">class </em><code class="descclassname">atomeye.</code><code class="descname">AtomEyeViewer</code><span class="sig-paren">(</span><em>atoms=None</em>, <em>viewer_id=None</em>, <em>copy=None</em>, <em>frame=0</em>, <em>delta=1</em>, <em>nowindow=False</em>, <em>echo=False</em>, <em>block=False</em>, <em>verbose=False</em>, <em>**showargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer" title="Permalink to this definition">¶</a></dt>
<dd><p>View an atomic configuration or trajectory with AtomEye</p>
<p>Class to represent an AtomEye viewer window. Each viewer class
communicates with one AtomEye thread.</p>
<p>There are wrapper methods for most of the <a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html#commands">AtomEye 3 commands</a>.
The names of these methods match the names of the correspondning
commands, and the arguments follow the syntax given on the AtomEye
3 help page.</p>
<p>Additional keyword arguments are passed along to the
<a class="reference internal" href="#atomeye.AtomEyeViewer.show" title="atomeye.AtomEyeViewer.show"><code class="xref py py-meth docutils literal notranslate"><span class="pre">show()</span></code></a> method.</p>
<p>Import <code class="xref py py-class docutils literal notranslate"><span class="pre">AtomEyeView</span></code> attributes:</p>
<dl class="attribute">
<dt id="atomeye.AtomEyeViewer.atoms">
<code class="descname">atoms</code><a class="headerlink" href="#atomeye.AtomEyeViewer.atoms" title="Permalink to this definition">¶</a></dt>
<dd><p><code class="xref py py-class docutils literal notranslate"><span class="pre">Atoms</span></code> object or sequence being viewed. This will be set
to <code class="docutils literal notranslate"><span class="pre">None</span></code> if this instance was created without an <code class="docutils literal notranslate"><span class="pre">obj</span></code>
parameter, which means we’re viewing the <code class="docutils literal notranslate"><span class="pre">A3</span></code> logo.</p>
</dd></dl>

<dl class="attribute">
<dt id="atomeye.AtomEyeViewer.frame">
<code class="descname">frame</code><a class="headerlink" href="#atomeye.AtomEyeViewer.frame" title="Permalink to this definition">¶</a></dt>
<dd><p>Current frame, in range 1 to <cite>len(self.atoms)</cite>.</p>
</dd></dl>

<dl class="attribute">
<dt id="atomeye.AtomEyeViewer.delta">
<code class="descname">delta</code><a class="headerlink" href="#atomeye.AtomEyeViewer.delta" title="Permalink to this definition">¶</a></dt>
<dd><p>Frame increment rate when <kbd class="kbd docutils literal notranslate">Delete</kbd> and <kbd class="kbd docutils literal notranslate">Insert</kbd> are
preseed. Equivalent to AtomEye <code class="docutils literal notranslate"><span class="pre">n-&gt;glob_advance</span></code> setting.</p>
</dd></dl>

<dl class="attribute">
<dt id="atomeye.AtomEyeViewer.echo">
<code class="descname">echo</code><a class="headerlink" href="#atomeye.AtomEyeViewer.echo" title="Permalink to this definition">¶</a></dt>
<dd><p>If set to True, echo all AtomEye commands to stdout</p>
</dd></dl>

<dl class="attribute">
<dt id="atomeye.AtomEyeViewer.block">
<code class="descname">block</code><a class="headerlink" href="#atomeye.AtomEyeViewer.block" title="Permalink to this definition">¶</a></dt>
<dd><p>If set to True, wait for all AtomEye command to finish
executing before returning from function calls. Default is
False.</p>
</dd></dl>

<dl class="attribute">
<dt id="atomeye.AtomEyeViewer.verbose">
<code class="descname">verbose</code><a class="headerlink" href="#atomeye.AtomEyeViewer.verbose" title="Permalink to this definition">¶</a></dt>
<dd><p>If set to True (default), print frame paramters on each
<a class="reference internal" href="#atomeye.redraw" title="atomeye.redraw"><code class="xref py py-meth docutils literal notranslate"><span class="pre">redraw()</span></code></a>, and print information about each atom when it is
right clicked.</p>
</dd></dl>

<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first docutils">
<dt><strong>atoms</strong> <span class="classifier-delimiter">:</span> <span class="classifier"><a class="reference internal" href="atoms.html#quippy.atoms.Atoms" title="quippy.atoms.Atoms"><code class="xref py py-class docutils literal notranslate"><span class="pre">quippy.atoms.Atoms</span></code></a> or <code class="xref py py-class docutils literal notranslate"><span class="pre">ase.atoms.Atoms</span></code> object, or a list of objects.</span></dt>
<dd><p class="first last">Configuration or trajectory to view.</p>
</dd>
<dt><strong>viewer_id</strong> <span class="classifier-delimiter">:</span> <span class="classifier">integer or None</span></dt>
<dd><p class="first last">If None, open a new viewer. Otherwise call the
:meth:show() method in the existing viewer with this ID.</p>
</dd>
<dt><strong>copy</strong> <span class="classifier-delimiter">:</span> <span class="classifier">integer or None</span></dt>
<dd><p class="first last">Viewer ID of another viewer from which to copy the viewpoint
and other default settings.</p>
</dd>
<dt><strong>frame</strong> <span class="classifier-delimiter">:</span> <span class="classifier">integer</span></dt>
<dd><p class="first last">Initial frame to show (should be in range <code class="docutils literal notranslate"><span class="pre">0..len(atoms)-1</span></code>)</p>
</dd>
<dt><strong>delta</strong> <span class="classifier-delimiter">:</span> <span class="classifier">integer</span></dt>
<dd><p class="first last">Increment/decrement rate for frames when [Insert] and [Delete]
are pressed</p>
</dd>
<dt><strong>nowindow</strong> <span class="classifier-delimiter">:</span> <span class="classifier">bool</span></dt>
<dd><p class="first last">If True, open AtomEye without a visible window. Useful
for faster rendering of movies</p>
</dd>
<dt><strong>echo</strong> <span class="classifier-delimiter">:</span> <span class="classifier">bool</span></dt>
<dd><p class="first last">If True, echo all commands to the screen.
Useful mainly for debugging.</p>
</dd>
<dt><strong>block</strong> <span class="classifier-delimiter">:</span> <span class="classifier">bool</span></dt>
<dd><p class="first last">If True, wait for commands to finish executing in AtomEye
thread before returning (i.e. run asynchronously)</p>
</dd>
<dt><strong>verbose</strong> <span class="classifier-delimiter">:</span> <span class="classifier">bool</span></dt>
<dd><p class="first last">If True, print information when changing frame and
when an atom is clicked</p>
</dd>
</dl>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Attributes:</th><td class="field-body"><dl class="first last docutils">
<dt><a class="reference internal" href="#atomeye.AtomEyeViewer.frame" title="atomeye.AtomEyeViewer.frame"><code class="xref py py-obj docutils literal notranslate"><span class="pre">frame</span></code></a></dt>
<dd><p class="first last">Get or set the current frame</p>
</dd>
</dl>
</td>
</tr>
</tbody>
</table>
<p class="rubric">Methods</p>
<table border="1" class="longtable docutils">
<colgroup>
<col width="10%" />
<col width="90%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.advance" title="atomeye.AtomEyeViewer.advance"><code class="xref py py-obj docutils literal notranslate"><span class="pre">advance</span></code></a>(delta)</td>
<td>Move the camera forward by <cite>delta</cite>.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.aux_property_coloring" title="atomeye.AtomEyeViewer.aux_property_coloring"><code class="xref py py-obj docutils literal notranslate"><span class="pre">aux_property_coloring</span></code></a>(auxprop)</td>
<td>Colour the atoms by the auxiliary property with name or index <cite>auxprop</cite>.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.backward" title="atomeye.AtomEyeViewer.backward"><code class="xref py py-obj docutils literal notranslate"><span class="pre">backward</span></code></a>([delta])</td>
<td>Move backward by <cite>delta</cite> frames (default values is self.delta).</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.capture" title="atomeye.AtomEyeViewer.capture"><code class="xref py py-obj docutils literal notranslate"><span class="pre">capture</span></code></a>(filename[,&nbsp;resolution])</td>
<td>Render the current view to image <cite>filename</cite></td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.central_symmetry_coloring" title="atomeye.AtomEyeViewer.central_symmetry_coloring"><code class="xref py py-obj docutils literal notranslate"><span class="pre">central_symmetry_coloring</span></code></a>()</td>
<td>Colour atoms by centro-symmetry parameter.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.change_atom_r_ratio" title="atomeye.AtomEyeViewer.change_atom_r_ratio"><code class="xref py py-obj docutils literal notranslate"><span class="pre">change_atom_r_ratio</span></code></a>(delta)</td>
<td>Change the size of the balls used to draw the atoms by <cite>delta</cite>.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.change_aux_colormap" title="atomeye.AtomEyeViewer.change_aux_colormap"><code class="xref py py-obj docutils literal notranslate"><span class="pre">change_aux_colormap</span></code></a>(n)</td>
<td>Select the <cite>n</cite>-th auxiliary property colourmap.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.change_aux_property_threshold" title="atomeye.AtomEyeViewer.change_aux_property_threshold"><code class="xref py py-obj docutils literal notranslate"><span class="pre">change_aux_property_threshold</span></code></a>(lower,&nbsp;upper)</td>
<td>Change the lower and upper aux property thresholds.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.change_bgcolor" title="atomeye.AtomEyeViewer.change_bgcolor"><code class="xref py py-obj docutils literal notranslate"><span class="pre">change_bgcolor</span></code></a>(color)</td>
<td>Change the viewer background colour to <cite>color</cite>, which should be a RGB tuple with three floats in range 0..1.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.change_bond_radius" title="atomeye.AtomEyeViewer.change_bond_radius"><code class="xref py py-obj docutils literal notranslate"><span class="pre">change_bond_radius</span></code></a>(delta)</td>
<td>Change the radius of the cylinders used the draw bonds by <cite>delta</cite>.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.close" title="atomeye.AtomEyeViewer.close"><code class="xref py py-obj docutils literal notranslate"><span class="pre">close</span></code></a>()</td>
<td>Close this viewer window.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.cutting_plane" title="atomeye.AtomEyeViewer.cutting_plane"><code class="xref py py-obj docutils literal notranslate"><span class="pre">cutting_plane</span></code></a>(n,&nbsp;d,&nbsp;s)</td>
<td>Create a new cutting plane with index <cite>n</cite>, normal <cite>d</cite>, and fractional displacement <cite>s</cite>.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.display" title="atomeye.AtomEyeViewer.display"><code class="xref py py-obj docutils literal notranslate"><span class="pre">display</span></code></a>()</td>
<td>Display snapshot from AtomEye session in IPython notebook</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.draw_arrows" title="atomeye.AtomEyeViewer.draw_arrows"><code class="xref py py-obj docutils literal notranslate"><span class="pre">draw_arrows</span></code></a>(property[,&nbsp;scale_factor,&nbsp;…])</td>
<td>Draw arrows on each atom, based on a vector property</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.find_atom" title="atomeye.AtomEyeViewer.find_atom"><code class="xref py py-obj docutils literal notranslate"><span class="pre">find_atom</span></code></a>(i)</td>
<td>Set the anchor to the atom with index <cite>i</cite>.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.first" title="atomeye.AtomEyeViewer.first"><code class="xref py py-obj docutils literal notranslate"><span class="pre">first</span></code></a>()</td>
<td>Show the first frame (frame 0).</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.forward" title="atomeye.AtomEyeViewer.forward"><code class="xref py py-obj docutils literal notranslate"><span class="pre">forward</span></code></a>([delta])</td>
<td>Move forward by <cite>delta</cite> frames (default value is self.delta).</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.gcat" title="atomeye.AtomEyeViewer.gcat"><code class="xref py py-obj docutils literal notranslate"><span class="pre">gcat</span></code></a>([update])</td>
<td>Get current atoms - return Atoms object currently being visualised.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.get_size_angstrom" title="atomeye.AtomEyeViewer.get_size_angstrom"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_size_angstrom</span></code></a>([state])</td>
<td>Return (width, height) in Angstrom of currently projected view</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.get_size_pixels" title="atomeye.AtomEyeViewer.get_size_pixels"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_size_pixels</span></code></a>([state])</td>
<td>Return (width, height) in pixels of this viewer</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.get_visible" title="atomeye.AtomEyeViewer.get_visible"><code class="xref py py-obj docutils literal notranslate"><span class="pre">get_visible</span></code></a>()</td>
<td>Return list of indices of atoms currently visible in this viewer.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.key" title="atomeye.AtomEyeViewer.key"><code class="xref py py-obj docutils literal notranslate"><span class="pre">key</span></code></a>(key)</td>
<td>Simulate pressing <cite>key</cite> on the keyboard.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.last" title="atomeye.AtomEyeViewer.last"><code class="xref py py-obj docutils literal notranslate"><span class="pre">last</span></code></a>()</td>
<td>Show the last frame, i.e.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.load_atom_color" title="atomeye.AtomEyeViewer.load_atom_color"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_atom_color</span></code></a>(filename)</td>
<td>Load atom colours from a .clr file.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.load_aux" title="atomeye.AtomEyeViewer.load_aux"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_aux</span></code></a>(filename)</td>
<td>Load aux property values from a .aux file.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.load_script" title="atomeye.AtomEyeViewer.load_script"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_script</span></code></a>(filename)</td>
<td>Load AtomEye viewer settings from a file using the AtomEye <code class="docutils literal notranslate"><span class="pre">load_script</span></code> command</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.normal_coloring" title="atomeye.AtomEyeViewer.normal_coloring"><code class="xref py py-obj docutils literal notranslate"><span class="pre">normal_coloring</span></code></a>()</td>
<td>Return to normal colouring of the atoms (key “o”).</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.rcut_patch" title="atomeye.AtomEyeViewer.rcut_patch"><code class="xref py py-obj docutils literal notranslate"><span class="pre">rcut_patch</span></code></a>(sym1,&nbsp;sym2,&nbsp;value[,&nbsp;absolute])</td>
<td>Change the cutoff distance for <cite>sym1</cite>–<cite>sym2</cite> bonds by <cite>delta</cite>.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.redraw" title="atomeye.AtomEyeViewer.redraw"><code class="xref py py-obj docutils literal notranslate"><span class="pre">redraw</span></code></a>()</td>
<td>Redraw this AtomEye window, keeping Atoms and settings the same.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.reset_aux_property_thresholds" title="atomeye.AtomEyeViewer.reset_aux_property_thresholds"><code class="xref py py-obj docutils literal notranslate"><span class="pre">reset_aux_property_thresholds</span></code></a>()</td>
<td>Reset aux property thresholds to automatic values.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.resize" title="atomeye.AtomEyeViewer.resize"><code class="xref py py-obj docutils literal notranslate"><span class="pre">resize</span></code></a>(width,&nbsp;height)</td>
<td>Resize the current window to <cite>width</cite> x <cite>height</cite> pixels.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.rotate" title="atomeye.AtomEyeViewer.rotate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">rotate</span></code></a>(axis,&nbsp;theta)</td>
<td>Rotate around <cite>axis</cite> by angle <cite>theta</cite>.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.run_command" title="atomeye.AtomEyeViewer.run_command"><code class="xref py py-obj docutils literal notranslate"><span class="pre">run_command</span></code></a>(command)</td>
<td>Run a command in this AtomEye thread.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.run_script" title="atomeye.AtomEyeViewer.run_script"><code class="xref py py-obj docutils literal notranslate"><span class="pre">run_script</span></code></a>(script)</td>
<td>Run commands from the file script, in a blocking fashion.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.save" title="atomeye.AtomEyeViewer.save"><code class="xref py py-obj docutils literal notranslate"><span class="pre">save</span></code></a>(filename)</td>
<td>Save AtomEye viewer settings to a file.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.scat" title="atomeye.AtomEyeViewer.scat"><code class="xref py py-obj docutils literal notranslate"><span class="pre">scat</span></code></a>(atoms[,&nbsp;frame])</td>
<td>Set current atoms (and optionally also current frame)</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.setp" title="atomeye.AtomEyeViewer.setp"><code class="xref py py-obj docutils literal notranslate"><span class="pre">setp</span></code></a>(key,&nbsp;value)</td>
<td>Run the AtomEye command “set key value”.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.shift_cutting_plane" title="atomeye.AtomEyeViewer.shift_cutting_plane"><code class="xref py py-obj docutils literal notranslate"><span class="pre">shift_cutting_plane</span></code></a>(delta)</td>
<td>Shift the current cutting plane by an amount <cite>delta</cite>.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.shift_xtal" title="atomeye.AtomEyeViewer.shift_xtal"><code class="xref py py-obj docutils literal notranslate"><span class="pre">shift_xtal</span></code></a>(axis,&nbsp;delta)</td>
<td>Shift crystal within periodic boundaries along <cite>axis</cite> by <cite>delta</cite> (key “Shift+left/right/up/down”).</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.show" title="atomeye.AtomEyeViewer.show"><code class="xref py py-obj docutils literal notranslate"><span class="pre">show</span></code></a>([atoms,&nbsp;property,&nbsp;frame,&nbsp;arrows])</td>
<td>Update what is shown in this AtomEye viewer window.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.start" title="atomeye.AtomEyeViewer.start"><code class="xref py py-obj docutils literal notranslate"><span class="pre">start</span></code></a>([copy,&nbsp;nowindow])</td>
<td>Start the AtomEye thread, wait for it to load and apply default commands.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.toggle_aux_property_thresholds_rigid" title="atomeye.AtomEyeViewer.toggle_aux_property_thresholds_rigid"><code class="xref py py-obj docutils literal notranslate"><span class="pre">toggle_aux_property_thresholds_rigid</span></code></a>()</td>
<td>Toggle between floating and rigid aux property thresholds when moving between frames</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.toggle_aux_property_thresholds_saturation" title="atomeye.AtomEyeViewer.toggle_aux_property_thresholds_saturation"><code class="xref py py-obj docutils literal notranslate"><span class="pre">toggle_aux_property_thresholds_saturation</span></code></a>()</td>
<td>Toggle between saturated colouring and invisibility for values outside aux prop thresholds.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.toggle_bond_mode" title="atomeye.AtomEyeViewer.toggle_bond_mode"><code class="xref py py-obj docutils literal notranslate"><span class="pre">toggle_bond_mode</span></code></a>()</td>
<td>Turn on or off bonds.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.toggle_coordination_coloring" title="atomeye.AtomEyeViewer.toggle_coordination_coloring"><code class="xref py py-obj docutils literal notranslate"><span class="pre">toggle_coordination_coloring</span></code></a>()</td>
<td>Turn on or off colouring by coordination number (key “k”)</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.toggle_parallel_projection" title="atomeye.AtomEyeViewer.toggle_parallel_projection"><code class="xref py py-obj docutils literal notranslate"><span class="pre">toggle_parallel_projection</span></code></a>()</td>
<td>Toggle between parallel and perspective projections.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.toggle_small_cell_mode" title="atomeye.AtomEyeViewer.toggle_small_cell_mode"><code class="xref py py-obj docutils literal notranslate"><span class="pre">toggle_small_cell_mode</span></code></a>()</td>
<td>Toggle between two different behaviours for when cell is smaller than r_cut/2:</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.translate" title="atomeye.AtomEyeViewer.translate"><code class="xref py py-obj docutils literal notranslate"><span class="pre">translate</span></code></a>(axis,&nbsp;delta)</td>
<td>Translate system along <cite>axis</cite> by an amount <cite>delta</cite> (key “Ctrl+left/right/up/down”)</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.update" title="atomeye.AtomEyeViewer.update"><code class="xref py py-obj docutils literal notranslate"><span class="pre">update</span></code></a>(state)</td>
<td>Update settings from the dictionary <cite>state</cite>.</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.wait" title="atomeye.AtomEyeViewer.wait"><code class="xref py py-obj docutils literal notranslate"><span class="pre">wait</span></code></a>()</td>
<td>Sleep until this AtomEye viewer has finished processing all queued events.</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="#atomeye.AtomEyeViewer.xtal_origin_goto" title="atomeye.AtomEyeViewer.xtal_origin_goto"><code class="xref py py-obj docutils literal notranslate"><span class="pre">xtal_origin_goto</span></code></a>(s)</td>
<td>Move the crystal origin to fractional coordinates <cite>s</cite></td>
</tr>
</tbody>
</table>
<dl class="method">
<dt id="atomeye.AtomEyeViewer.advance">
<code class="descname">advance</code><span class="sig-paren">(</span><em>delta</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.advance"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.advance" title="Permalink to this definition">¶</a></dt>
<dd><p>Move the camera forward by <cite>delta</cite>.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.aux_property_coloring">
<code class="descname">aux_property_coloring</code><span class="sig-paren">(</span><em>auxprop</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.aux_property_coloring"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.aux_property_coloring" title="Permalink to this definition">¶</a></dt>
<dd><p>Colour the atoms by the auxiliary property with name or index <cite>auxprop</cite>.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.backward">
<code class="descname">backward</code><span class="sig-paren">(</span><em>delta=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.backward"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.backward" title="Permalink to this definition">¶</a></dt>
<dd><p>Move backward by <cite>delta</cite> frames (default values is self.delta).</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.capture">
<code class="descname">capture</code><span class="sig-paren">(</span><em>filename</em>, <em>resolution=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.capture"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.capture" title="Permalink to this definition">¶</a></dt>
<dd><p>Render the current view to image <cite>filename</cite></p>
<p>Format is determined from file extension: .png, .jpeg, or .eps.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.central_symmetry_coloring">
<code class="descname">central_symmetry_coloring</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.central_symmetry_coloring"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.central_symmetry_coloring" title="Permalink to this definition">¶</a></dt>
<dd><p>Colour atoms by centro-symmetry parameter.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.change_atom_r_ratio">
<code class="descname">change_atom_r_ratio</code><span class="sig-paren">(</span><em>delta</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.change_atom_r_ratio"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.change_atom_r_ratio" title="Permalink to this definition">¶</a></dt>
<dd><p>Change the size of the balls used to draw the atoms by <cite>delta</cite>.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.change_aux_colormap">
<code class="descname">change_aux_colormap</code><span class="sig-paren">(</span><em>n</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.change_aux_colormap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.change_aux_colormap" title="Permalink to this definition">¶</a></dt>
<dd><p>Select the <cite>n</cite>-th auxiliary property colourmap.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.change_aux_property_threshold">
<code class="descname">change_aux_property_threshold</code><span class="sig-paren">(</span><em>lower</em>, <em>upper</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.change_aux_property_threshold"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.change_aux_property_threshold" title="Permalink to this definition">¶</a></dt>
<dd><p>Change the lower and upper aux property thresholds.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.change_bgcolor">
<code class="descname">change_bgcolor</code><span class="sig-paren">(</span><em>color</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.change_bgcolor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.change_bgcolor" title="Permalink to this definition">¶</a></dt>
<dd><p>Change the viewer background colour to <cite>color</cite>, which should be a RGB tuple with three floats in range 0..1.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.change_bond_radius">
<code class="descname">change_bond_radius</code><span class="sig-paren">(</span><em>delta</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.change_bond_radius"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.change_bond_radius" title="Permalink to this definition">¶</a></dt>
<dd><p>Change the radius of the cylinders used the draw bonds by <cite>delta</cite>.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.close">
<code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.close" title="Permalink to this definition">¶</a></dt>
<dd><p>Close this viewer window.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.cutting_plane">
<code class="descname">cutting_plane</code><span class="sig-paren">(</span><em>n</em>, <em>d</em>, <em>s</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.cutting_plane"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.cutting_plane" title="Permalink to this definition">¶</a></dt>
<dd><p>Create a new cutting plane with index <cite>n</cite>, normal <cite>d</cite>, and fractional displacement <cite>s</cite>.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.display">
<code class="descname">display</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.display"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.display" title="Permalink to this definition">¶</a></dt>
<dd><p>Display snapshot from AtomEye session in IPython notebook</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.draw_arrows">
<code class="descname">draw_arrows</code><span class="sig-paren">(</span><em>property</em>, <em>scale_factor=0.0</em>, <em>head_height=0.1</em>, <em>head_width=0.05</em>, <em>up=(0.0</em>, <em>1.0</em>, <em>0.0)</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.draw_arrows"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.draw_arrows" title="Permalink to this definition">¶</a></dt>
<dd><p>Draw arrows on each atom, based on a vector property</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>property</strong> <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
<dd><p class="first last">Name of the array to use for arrow vectors.
Use <code class="docutils literal notranslate"><span class="pre">None</span></code> to turn off previous arrows.</p>
</dd>
<dt><strong>scale_factor</strong> <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
<dd><p class="first last">Override length of arrows. 1 unit = 1 Angstrom; default
value of 0.0 means autoscale.</p>
</dd>
<dt><strong>head_height</strong> <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
<dd><p class="first last">Specify height of arrow heads in Angstrom.</p>
</dd>
<dt><strong>head_width</strong> <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
<dd></dd>
<dt><strong>up</strong> <span class="classifier-delimiter">:</span> <span class="classifier">3-vector (tuple, list or array)</span></dt>
<dd><p class="first last">Specify the plane in which the arrow heads are
drawn. Arrows are drawn in the plane which is common
to their direction and this vector.
Default is <code class="docutils literal notranslate"><span class="pre">[0.,1.,0.]</span></code>.</p>
</dd>
</dl>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.find_atom">
<code class="descname">find_atom</code><span class="sig-paren">(</span><em>i</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.find_atom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.find_atom" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the anchor to the atom with index <cite>i</cite>.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.first">
<code class="descname">first</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.first"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.first" title="Permalink to this definition">¶</a></dt>
<dd><p>Show the first frame (frame 0).</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.forward">
<code class="descname">forward</code><span class="sig-paren">(</span><em>delta=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.forward"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.forward" title="Permalink to this definition">¶</a></dt>
<dd><p>Move forward by <cite>delta</cite> frames (default value is self.delta).</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.gcat">
<code class="descname">gcat</code><span class="sig-paren">(</span><em>update=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.gcat"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.gcat" title="Permalink to this definition">¶</a></dt>
<dd><p>Get current atoms - return Atoms object currently being visualised.</p>
<p>If update=False (the default), we return what is currently being visualised,
even if this is not in sync with self.atoms[self.frame].</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.get_size_angstrom">
<code class="descname">get_size_angstrom</code><span class="sig-paren">(</span><em>state=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.get_size_angstrom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.get_size_angstrom" title="Permalink to this definition">¶</a></dt>
<dd><p>Return (width, height) in Angstrom of currently projected view</p>
<p>Assumes object lies in plane z=0</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.get_size_pixels">
<code class="descname">get_size_pixels</code><span class="sig-paren">(</span><em>state=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.get_size_pixels"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.get_size_pixels" title="Permalink to this definition">¶</a></dt>
<dd><p>Return (width, height) in pixels of this viewer</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.get_visible">
<code class="descname">get_visible</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.get_visible"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.get_visible" title="Permalink to this definition">¶</a></dt>
<dd><p>Return list of indices of atoms currently visible in this viewer.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.key">
<code class="descname">key</code><span class="sig-paren">(</span><em>key</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.key"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.key" title="Permalink to this definition">¶</a></dt>
<dd><p>Simulate pressing <cite>key</cite> on the keyboard.</p>
<p>The syntax for keystrokes is described on the <a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html#commands">AtomEye 3
commands help page</a></p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.last">
<code class="descname">last</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.last"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.last" title="Permalink to this definition">¶</a></dt>
<dd><p>Show the last frame, i.e. len(self.atoms)-1</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.load_atom_color">
<code class="descname">load_atom_color</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.load_atom_color"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.load_atom_color" title="Permalink to this definition">¶</a></dt>
<dd><p>Load atom colours from a .clr file.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.load_aux">
<code class="descname">load_aux</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.load_aux"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.load_aux" title="Permalink to this definition">¶</a></dt>
<dd><p>Load aux property values from a .aux file.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.load_script">
<code class="descname">load_script</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.load_script"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.load_script" title="Permalink to this definition">¶</a></dt>
<dd><p>Load AtomEye viewer settings from a file using the AtomEye <code class="docutils literal notranslate"><span class="pre">load_script</span></code> command</p>
<p><a class="reference internal" href="#atomeye.run_script" title="atomeye.run_script"><code class="xref py py-meth docutils literal notranslate"><span class="pre">run_script()</span></code></a> is more robust as the script is run line by
line in a blocking sense.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.normal_coloring">
<code class="descname">normal_coloring</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.normal_coloring"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.normal_coloring" title="Permalink to this definition">¶</a></dt>
<dd><p>Return to normal colouring of the atoms (key “o”).</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.rcut_patch">
<code class="descname">rcut_patch</code><span class="sig-paren">(</span><em>sym1</em>, <em>sym2</em>, <em>value</em>, <em>absolute=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.rcut_patch"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.rcut_patch" title="Permalink to this definition">¶</a></dt>
<dd><p>Change the cutoff distance for <cite>sym1</cite>–<cite>sym2</cite> bonds by <cite>delta</cite>.</p>
<p>e.g. to increase cutoff for Si-Si bonds by 0.5 A use:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">viewer</span><span class="o">.</span><span class="n">rcut_patch</span><span class="p">(</span><span class="s1">&#39;Si&#39;</span><span class="p">,</span> <span class="s1">&#39;Si&#39;</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">)</span>
</pre></div>
</div>
<p>With <cite>absolute</cite> set to True, <cite>value</cite> is used to set the
absolute cutoff distance for <cite>sym1</cite>–<cite>sym2</cite> bonds, e.g.:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">viewer</span><span class="o">.</span><span class="n">rcut_patch</span><span class="p">(</span><span class="s1">&#39;Si&#39;</span><span class="p">,</span> <span class="s1">&#39;Si&#39;</span><span class="p">,</span> <span class="mf">2.50</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
</pre></div>
</div>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.redraw">
<code class="descname">redraw</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.redraw"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.redraw" title="Permalink to this definition">¶</a></dt>
<dd><p>Redraw this AtomEye window, keeping Atoms and settings the same.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.reset_aux_property_thresholds">
<code class="descname">reset_aux_property_thresholds</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.reset_aux_property_thresholds"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.reset_aux_property_thresholds" title="Permalink to this definition">¶</a></dt>
<dd><p>Reset aux property thresholds to automatic values.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.resize">
<code class="descname">resize</code><span class="sig-paren">(</span><em>width</em>, <em>height</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.resize"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.resize" title="Permalink to this definition">¶</a></dt>
<dd><p>Resize the current window to <cite>width</cite> x <cite>height</cite> pixels.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.rotate">
<code class="descname">rotate</code><span class="sig-paren">(</span><em>axis</em>, <em>theta</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.rotate"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.rotate" title="Permalink to this definition">¶</a></dt>
<dd><p>Rotate around <cite>axis</cite> by angle <cite>theta</cite>.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.run_command">
<code class="descname">run_command</code><span class="sig-paren">(</span><em>command</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.run_command"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.run_command" title="Permalink to this definition">¶</a></dt>
<dd><p>Run a command in this AtomEye thread.</p>
<p>The command is queued for later execution, unless <a class="reference internal" href="#atomeye.AtomEyeViewer.block" title="atomeye.AtomEyeViewer.block"><code class="xref py py-attr docutils literal notranslate"><span class="pre">block</span></code></a> is True.</p>
<p>This functionality is also available by calling an instance
directly, i.e. the following commands are equivalent:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">viewer</span><span class="o">.</span><span class="n">run_command</span><span class="p">(</span><span class="s1">&#39;toggle_coordination_coloring&#39;</span><span class="p">)</span>
<span class="n">viewer</span><span class="p">(</span><span class="s1">&#39;toggle_coordination_coloring&#39;</span><span class="p">)</span>
</pre></div>
</div>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>command</strong> <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
<dd><p class="first last">The command to pass to AtomEye</p>
</dd>
</dl>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.run_script">
<code class="descname">run_script</code><span class="sig-paren">(</span><em>script</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.run_script"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.run_script" title="Permalink to this definition">¶</a></dt>
<dd><p>Run commands from the file script, in a blocking fashion.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.save">
<code class="descname">save</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.save"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.save" title="Permalink to this definition">¶</a></dt>
<dd><p>Save AtomEye viewer settings to a file.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.scat">
<code class="descname">scat</code><span class="sig-paren">(</span><em>atoms</em>, <em>frame=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.scat"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.scat" title="Permalink to this definition">¶</a></dt>
<dd><p>Set current atoms (and optionally also current frame)</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.setp">
<code class="descname">setp</code><span class="sig-paren">(</span><em>key</em>, <em>value</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.setp"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.setp" title="Permalink to this definition">¶</a></dt>
<dd><p>Run the AtomEye command “set key value”.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.shift_cutting_plane">
<code class="descname">shift_cutting_plane</code><span class="sig-paren">(</span><em>delta</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.shift_cutting_plane"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.shift_cutting_plane" title="Permalink to this definition">¶</a></dt>
<dd><p>Shift the current cutting plane by an amount <cite>delta</cite>.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.shift_xtal">
<code class="descname">shift_xtal</code><span class="sig-paren">(</span><em>axis</em>, <em>delta</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.shift_xtal"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.shift_xtal" title="Permalink to this definition">¶</a></dt>
<dd><p>Shift crystal within periodic boundaries along <cite>axis</cite> by <cite>delta</cite> (key “Shift+left/right/up/down”).</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.show">
<code class="descname">show</code><span class="sig-paren">(</span><em>atoms=None</em>, <em>property=None</em>, <em>frame=None</em>, <em>arrows=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.show"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.show" title="Permalink to this definition">¶</a></dt>
<dd><p>Update what is shown in this AtomEye viewer window.</p>
<p>When called with no arguments, <a class="reference internal" href="#atomeye.AtomEyeViewer.show" title="atomeye.AtomEyeViewer.show"><code class="xref py py-meth docutils literal notranslate"><span class="pre">show()</span></code></a> is equivalent to
<a class="reference internal" href="#atomeye.redraw" title="atomeye.redraw"><code class="xref py py-meth docutils literal notranslate"><span class="pre">redraw()</span></code></a>.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>atoms</strong> <span class="classifier-delimiter">:</span> <span class="classifier">class:<cite>quippy.atoms.Atoms or `ase.atoms.Atoms</cite></span></dt>
<dd><p class="first last">instance, or a list of instances</p>
</dd>
<dt><strong>property</strong> <span class="classifier-delimiter">:</span> <span class="classifier">name of the quippy :<code class="docutils literal notranslate"><span class="pre">~quippy.atoms.properties</span></code></span></dt>
<dd><p class="first last">entry or ASE <code class="xref py py-attr docutils literal notranslate"><span class="pre">ase.atoms.arrays</span></code> entry used to
colour the atoms (e.g. <code class="docutils literal notranslate"><span class="pre">&quot;charge&quot;</span></code>)</p>
</dd>
<dt><strong>frame</strong> <span class="classifier-delimiter">:</span> <span class="classifier">Zero-based index of the frame to show</span></dt>
<dd><p class="first last">(applies only when <cite>atoms</cite> is a list of Atoms objects)</p>
</dd>
<dt><strong>arrows</strong> <span class="classifier-delimiter">:</span> <span class="classifier">is the name of a vector property to use to draw arrows</span></dt>
<dd><p class="first last">on the atoms (e.g. <code class="docutils literal notranslate"><span class="pre">&quot;force&quot;</span></code>)</p>
</dd>
</dl>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.start">
<code class="descname">start</code><span class="sig-paren">(</span><em>copy=None</em>, <em>nowindow=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.start"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.start" title="Permalink to this definition">¶</a></dt>
<dd><p>Start the AtomEye thread, wait for it to load and apply
default commands.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>copy</strong> <span class="classifier-delimiter">:</span> <span class="classifier">integer</span></dt>
<dd><p class="first last">Viewer ID of another AtomEye window from which to
copy settings</p>
</dd>
<dt><strong>nowindow</strong> <span class="classifier-delimiter">:</span> <span class="classifier">bool</span></dt>
<dd><p class="first last">If True, create an AtomEye thread without a visible
window. Useful for rendering movies.</p>
</dd>
</dl>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.toggle_aux_property_thresholds_rigid">
<code class="descname">toggle_aux_property_thresholds_rigid</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.toggle_aux_property_thresholds_rigid"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.toggle_aux_property_thresholds_rigid" title="Permalink to this definition">¶</a></dt>
<dd><p>Toggle between floating and rigid aux property thresholds when moving between frames</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.toggle_aux_property_thresholds_saturation">
<code class="descname">toggle_aux_property_thresholds_saturation</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.toggle_aux_property_thresholds_saturation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.toggle_aux_property_thresholds_saturation" title="Permalink to this definition">¶</a></dt>
<dd><p>Toggle between saturated colouring and invisibility for values outside aux prop thresholds.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.toggle_bond_mode">
<code class="descname">toggle_bond_mode</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.toggle_bond_mode"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.toggle_bond_mode" title="Permalink to this definition">¶</a></dt>
<dd><p>Turn on or off bonds.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.toggle_coordination_coloring">
<code class="descname">toggle_coordination_coloring</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.toggle_coordination_coloring"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.toggle_coordination_coloring" title="Permalink to this definition">¶</a></dt>
<dd><p>Turn on or off colouring by coordination number (key “k”)</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.toggle_parallel_projection">
<code class="descname">toggle_parallel_projection</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.toggle_parallel_projection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.toggle_parallel_projection" title="Permalink to this definition">¶</a></dt>
<dd><p>Toggle between parallel and perspective projections.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.toggle_small_cell_mode">
<code class="descname">toggle_small_cell_mode</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.toggle_small_cell_mode"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.toggle_small_cell_mode" title="Permalink to this definition">¶</a></dt>
<dd><dl class="docutils">
<dt>Toggle between two different behaviours for when cell is smaller than r_cut/2:</dt>
<dd><ol class="first last arabic simple">
<li>clip cell - some neigbours may be lost (default)</li>
<li>replicate cell along narrow directions</li>
</ol>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.translate">
<code class="descname">translate</code><span class="sig-paren">(</span><em>axis</em>, <em>delta</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.translate"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.translate" title="Permalink to this definition">¶</a></dt>
<dd><p>Translate system along <cite>axis</cite> by an amount <cite>delta</cite> (key “Ctrl+left/right/up/down”)</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.update">
<code class="descname">update</code><span class="sig-paren">(</span><em>state</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.update"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.update" title="Permalink to this definition">¶</a></dt>
<dd><p>Update settings from the dictionary <cite>state</cite>.</p>
<p>Runs the AtomEye command <code class="docutils literal notranslate"><span class="pre">set</span> <span class="pre">key</span> <span class="pre">value</span></code> for each pair. Valid settings
are listed on the <a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A3/A3.html#redraw">AtomEye 3 settings help page</a></p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.wait">
<code class="descname">wait</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.wait"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.wait" title="Permalink to this definition">¶</a></dt>
<dd><p>Sleep until this AtomEye viewer has finished processing all queued events.</p>
</dd></dl>

<dl class="method">
<dt id="atomeye.AtomEyeViewer.xtal_origin_goto">
<code class="descname">xtal_origin_goto</code><span class="sig-paren">(</span><em>s</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#AtomEyeViewer.xtal_origin_goto"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.AtomEyeViewer.xtal_origin_goto" title="Permalink to this definition">¶</a></dt>
<dd><p>Move the crystal origin to fractional coordinates <cite>s</cite></p>
<p>For example, use <code class="docutils literal notranslate"><span class="pre">s=[0.5,</span> <span class="pre">0.5,</span> <span class="pre">0.5]</span></code> to shift by half the cell along
the <span class="math notranslate nohighlight">\(\mathbf{a}\)</span>, <span class="math notranslate nohighlight">\(\mathbf{b}\)</span> and <span class="math notranslate nohighlight">\(\mathbf{c}\)</span>
lattice vectors.</p>
</dd></dl>

<dl class="attribute">
<dt>
<code class="descname">frame</code></dt>
<dd><p>Get or set the current frame</p>
</dd></dl>

</dd></dl>

<dl class="function">
<dt id="atomeye.view">
<code class="descclassname">atomeye.</code><code class="descname">view</code><span class="sig-paren">(</span><em>atoms</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#view"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.view" title="Permalink to this definition">¶</a></dt>
<dd><p>Convenience wrapper to create/reuse a default <cite>AtomEyeViewer</cite></p>
</dd></dl>

<dl class="function">
<dt id="atomeye.redraw">
<code class="descclassname">atomeye.</code><code class="descname">redraw</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#redraw"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.redraw" title="Permalink to this definition">¶</a></dt>
<dd><p>Redraw current AtomEye window, keeping Atoms and settings the same.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.run_command">
<code class="descclassname">atomeye.</code><code class="descname">run_command</code><span class="sig-paren">(</span><em>command</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#run_command"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.run_command" title="Permalink to this definition">¶</a></dt>
<dd><p>Run a command in current AtomEye thread.</p>
<p>The command is queued for later execution, unless <code class="xref py py-attr docutils literal notranslate"><span class="pre">block</span></code> is True.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>command</strong> <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
<dd><p class="first last">The command to pass to AtomEye</p>
</dd>
</dl>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="function">
<dt id="atomeye.run_script">
<code class="descclassname">atomeye.</code><code class="descname">run_script</code><span class="sig-paren">(</span><em>script</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#run_script"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.run_script" title="Permalink to this definition">¶</a></dt>
<dd><p>Run commands from the file script, in a blocking fashion.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.close">
<code class="descclassname">atomeye.</code><code class="descname">close</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#close"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.close" title="Permalink to this definition">¶</a></dt>
<dd><p>Close the current viewer window.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.setp">
<code class="descclassname">atomeye.</code><code class="descname">setp</code><span class="sig-paren">(</span><em>self</em>, <em>key</em>, <em>value</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#setp"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.setp" title="Permalink to this definition">¶</a></dt>
<dd><p>Run the AtomEye command “set key value”</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.save_script">
<code class="descclassname">atomeye.</code><code class="descname">save_script</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#save_script"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.save_script" title="Permalink to this definition">¶</a></dt>
<dd><p>Save AtomEye viewer settings to a file.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.toggle_coordination_coloring">
<code class="descclassname">atomeye.</code><code class="descname">toggle_coordination_coloring</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#toggle_coordination_coloring"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.toggle_coordination_coloring" title="Permalink to this definition">¶</a></dt>
<dd><p>Turn on or off colouring by coordination number (key “k”)</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.translate">
<code class="descclassname">atomeye.</code><code class="descname">translate</code><span class="sig-paren">(</span><em>axis</em>, <em>delta</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#translate"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.translate" title="Permalink to this definition">¶</a></dt>
<dd><p>Translate system along <cite>axis</cite> by an amount <cite>delta</cite> (key “Ctrl+left/right/up/down”)</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.shift_xtal">
<code class="descclassname">atomeye.</code><code class="descname">shift_xtal</code><span class="sig-paren">(</span><em>axis</em>, <em>delta</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#shift_xtal"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.shift_xtal" title="Permalink to this definition">¶</a></dt>
<dd><p>Shift crystal within periodic boundaries along <cite>axis</cite> by <cite>delta</cite> (key “Shift+left/right/up/down”).</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.rotate">
<code class="descclassname">atomeye.</code><code class="descname">rotate</code><span class="sig-paren">(</span><em>axis</em>, <em>theta</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#rotate"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.rotate" title="Permalink to this definition">¶</a></dt>
<dd><p>Rotate around <cite>axis</cite> by angle <cite>theta</cite>.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.advance">
<code class="descclassname">atomeye.</code><code class="descname">advance</code><span class="sig-paren">(</span><em>delta</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#advance"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.advance" title="Permalink to this definition">¶</a></dt>
<dd><p>Move the camera forward by <cite>delta</cite>.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.shift_cutting_plane">
<code class="descclassname">atomeye.</code><code class="descname">shift_cutting_plane</code><span class="sig-paren">(</span><em>delta</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#shift_cutting_plane"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.shift_cutting_plane" title="Permalink to this definition">¶</a></dt>
<dd><p>Shift the current cutting plane by an amount <cite>delta</cite>.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.change_bgcolor">
<code class="descclassname">atomeye.</code><code class="descname">change_bgcolor</code><span class="sig-paren">(</span><em>color</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#change_bgcolor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.change_bgcolor" title="Permalink to this definition">¶</a></dt>
<dd><p>Change the viewer background colour to <cite>color</cite>, which should be a RGB tuple with three floats in range 0..1.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.change_atom_r_ratio">
<code class="descclassname">atomeye.</code><code class="descname">change_atom_r_ratio</code><span class="sig-paren">(</span><em>delta</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#change_atom_r_ratio"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.change_atom_r_ratio" title="Permalink to this definition">¶</a></dt>
<dd><p>Change the size of the balls used to draw the atoms by <cite>delta</cite>.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.change_bond_radius">
<code class="descclassname">atomeye.</code><code class="descname">change_bond_radius</code><span class="sig-paren">(</span><em>delta</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#change_bond_radius"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.change_bond_radius" title="Permalink to this definition">¶</a></dt>
<dd><p>Change the radius of the cylinders used the draw bonds by <cite>delta</cite>.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.change_view_angle_amplification">
<code class="descclassname">atomeye.</code><code class="descname">change_view_angle_amplification</code><span class="sig-paren">(</span><em>delta</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#change_view_angle_amplification"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.change_view_angle_amplification" title="Permalink to this definition">¶</a></dt>
<dd><p>Change the amplification of the view angle by <cite>delta</cite>.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.toggle_parallel_projection">
<code class="descclassname">atomeye.</code><code class="descname">toggle_parallel_projection</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#toggle_parallel_projection"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.toggle_parallel_projection" title="Permalink to this definition">¶</a></dt>
<dd><p>Toggle between parallel and perspective projections.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.toggle_bond_mode">
<code class="descclassname">atomeye.</code><code class="descname">toggle_bond_mode</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#toggle_bond_mode"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.toggle_bond_mode" title="Permalink to this definition">¶</a></dt>
<dd><p>Turn on or off bonds.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.toggle_small_cell_mode">
<code class="descclassname">atomeye.</code><code class="descname">toggle_small_cell_mode</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#toggle_small_cell_mode"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.toggle_small_cell_mode" title="Permalink to this definition">¶</a></dt>
<dd><dl class="docutils">
<dt>Toggle between two different behaviours for when cell is smaller than r_cut/2:</dt>
<dd><ol class="first last arabic simple">
<li>clip cell - some neigbours may be lost (default)</li>
<li>replicate cell along narrow directions</li>
</ol>
</dd>
</dl>
</dd></dl>

<dl class="function">
<dt id="atomeye.normal_coloring">
<code class="descclassname">atomeye.</code><code class="descname">normal_coloring</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#normal_coloring"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.normal_coloring" title="Permalink to this definition">¶</a></dt>
<dd><p>Return to normal colouring of the atoms (key “o”).</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.aux_property_coloring">
<code class="descclassname">atomeye.</code><code class="descname">aux_property_coloring</code><span class="sig-paren">(</span><em>auxprop</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#aux_property_coloring"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.aux_property_coloring" title="Permalink to this definition">¶</a></dt>
<dd><p>Colour the currently viewed atoms according to <cite>auxprop</cite>.</p>
<p>Overloaded to allow 
See <a class="reference internal" href="qlab.html#qlab-atom-coloring"><span class="std std-ref">Custom Atom Colouring</span></a> for more details and examples.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>auxprop</strong> <span class="classifier-delimiter">:</span> <span class="classifier">str, array_like, int or list</span></dt>
<dd><p class="first last">Values to use to colour the atoms. Should be either the
name of a scalar field entry in <a class="reference internal" href="atoms.html#quippy.atoms.Atoms.properties" title="quippy.atoms.Atoms.properties"><code class="xref py py-attr docutils literal notranslate"><span class="pre">properties</span></code></a>
(or equivalently, <code class="xref py py-attr docutils literal notranslate"><span class="pre">arrays</span></code>) such as <code class="docutils literal notranslate"><span class="pre">&quot;charge&quot;</span></code>,
a float, int or bool array of shape <code class="docutils literal notranslate"><span class="pre">(len(gcat()),)</span></code>, or an
atom index or list of atom indices to highlight particular atoms.</p>
</dd>
</dl>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="function">
<dt id="atomeye.central_symmetry_coloring">
<code class="descclassname">atomeye.</code><code class="descname">central_symmetry_coloring</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#central_symmetry_coloring"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.central_symmetry_coloring" title="Permalink to this definition">¶</a></dt>
<dd><p>Colour atoms by centro-symmetry parameter.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.change_aux_property_threshold">
<code class="descclassname">atomeye.</code><code class="descname">change_aux_property_threshold</code><span class="sig-paren">(</span><em>lower</em>, <em>upper</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#change_aux_property_threshold"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.change_aux_property_threshold" title="Permalink to this definition">¶</a></dt>
<dd><p>Change the lower and upper aux property thresholds.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.reset_aux_property_thresholds">
<code class="descclassname">atomeye.</code><code class="descname">reset_aux_property_thresholds</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#reset_aux_property_thresholds"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.reset_aux_property_thresholds" title="Permalink to this definition">¶</a></dt>
<dd><p>Reset aux property thresholds to automatic values.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.toggle_aux_property_thresholds_saturation">
<code class="descclassname">atomeye.</code><code class="descname">toggle_aux_property_thresholds_saturation</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#toggle_aux_property_thresholds_saturation"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.toggle_aux_property_thresholds_saturation" title="Permalink to this definition">¶</a></dt>
<dd><p>Toggle between saturated colouring and invisibility for values outside aux prop thresholds.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.toggle_aux_property_thresholds_rigid">
<code class="descclassname">atomeye.</code><code class="descname">toggle_aux_property_thresholds_rigid</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#toggle_aux_property_thresholds_rigid"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.toggle_aux_property_thresholds_rigid" title="Permalink to this definition">¶</a></dt>
<dd><p>Toggle between floating and rigid aux property thresholds when moving between frames</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.rcut_patch">
<code class="descclassname">atomeye.</code><code class="descname">rcut_patch</code><span class="sig-paren">(</span><em>sym1</em>, <em>sym2</em>, <em>value</em>, <em>absolute=False</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#rcut_patch"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.rcut_patch" title="Permalink to this definition">¶</a></dt>
<dd><p>Change the cutoff distance for <cite>sym1</cite>–<cite>sym2</cite> bonds by <cite>delta</cite>.</p>
<p>e.g. to increase cutoff for Si-Si bonds by 0.5 A use:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">viewer</span><span class="o">.</span><span class="n">rcut_patch</span><span class="p">(</span><span class="s1">&#39;Si&#39;</span><span class="p">,</span> <span class="s1">&#39;Si&#39;</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">)</span>
</pre></div>
</div>
<p>With <cite>absolute</cite> set to True, <cite>value</cite> is used to set the
absolute cutoff distance for <cite>sym1</cite>–<cite>sym2</cite> bonds, e.g.:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">viewer</span><span class="o">.</span><span class="n">rcut_patch</span><span class="p">(</span><span class="s1">&#39;Si&#39;</span><span class="p">,</span> <span class="s1">&#39;Si&#39;</span><span class="p">,</span> <span class="mf">2.50</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span>
</pre></div>
</div>
</dd></dl>

<dl class="function">
<dt id="atomeye.select_gear">
<code class="descclassname">atomeye.</code><code class="descname">select_gear</code><span class="sig-paren">(</span><em>gear</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#select_gear"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.select_gear" title="Permalink to this definition">¶</a></dt>
<dd><p>Change the AtomEye gear to <cite>gear</cite></p>
<p>Equivalent to pressing the one of the numeric keys 0..9</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.cutting_plane">
<code class="descclassname">atomeye.</code><code class="descname">cutting_plane</code><span class="sig-paren">(</span><em>n</em>, <em>d</em>, <em>s</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#cutting_plane"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.cutting_plane" title="Permalink to this definition">¶</a></dt>
<dd><p>Create a new cutting plane with index <cite>n</cite>, normal <cite>d</cite>, and fractional displacement <cite>s</cite>.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.shift_cutting_plane_to_anchor">
<code class="descclassname">atomeye.</code><code class="descname">shift_cutting_plane_to_anchor</code><span class="sig-paren">(</span><em>n</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#shift_cutting_plane_to_anchor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.shift_cutting_plane_to_anchor" title="Permalink to this definition">¶</a></dt>
<dd><p>Move the cutting plane with index <cite>n</cite> to the anchor</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.delete_cutting_plane">
<code class="descclassname">atomeye.</code><code class="descname">delete_cutting_plane</code><span class="sig-paren">(</span><em>n</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#delete_cutting_plane"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.delete_cutting_plane" title="Permalink to this definition">¶</a></dt>
<dd><p>Delete the cutting plane with index <cite>n</cite></p>
</dd></dl>

<dl class="function">
<dt id="atomeye.flip_cutting_plane">
<code class="descclassname">atomeye.</code><code class="descname">flip_cutting_plane</code><span class="sig-paren">(</span><em>n</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#flip_cutting_plane"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.flip_cutting_plane" title="Permalink to this definition">¶</a></dt>
<dd><p>Flip the cutting plane with index <cite>n</cite></p>
</dd></dl>

<dl class="function">
<dt id="atomeye.capture">
<code class="descclassname">atomeye.</code><code class="descname">capture</code><span class="sig-paren">(</span><em>filename</em>, <em>resolution=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#capture"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.capture" title="Permalink to this definition">¶</a></dt>
<dd><p>Render the current view to image <cite>filename</cite></p>
<p>Format is determined from file extension: .png, .jpeg, or .eps.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.change_wireframe_mode">
<code class="descclassname">atomeye.</code><code class="descname">change_wireframe_mode</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#change_wireframe_mode"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.change_wireframe_mode" title="Permalink to this definition">¶</a></dt>
<dd><p>Change the display mode for the unit cell box.</p>
<p>Equivalent to pressing the <cite>i</cite> key.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.change_cutting_plane_wireframe_mode">
<code class="descclassname">atomeye.</code><code class="descname">change_cutting_plane_wireframe_mode</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#change_cutting_plane_wireframe_mode"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.change_cutting_plane_wireframe_mode" title="Permalink to this definition">¶</a></dt>
<dd><p>Change the display mode for cutting planes</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.get_frame">
<code class="descclassname">atomeye.</code><code class="descname">get_frame</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#get_frame"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.get_frame" title="Permalink to this definition">¶</a></dt>
<dd><p>Get index of frame currently being viewed</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.set_frame">
<code class="descclassname">atomeye.</code><code class="descname">set_frame</code><span class="sig-paren">(</span><em>frame</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#set_frame"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.set_frame" title="Permalink to this definition">¶</a></dt>
<dd><p>Set current frame index to <cite>frame</cite></p>
</dd></dl>

<dl class="function">
<dt id="atomeye.get_delta">
<code class="descclassname">atomeye.</code><code class="descname">get_delta</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#get_delta"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.get_delta" title="Permalink to this definition">¶</a></dt>
<dd><p>Get frame increment rate</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.set_delta">
<code class="descclassname">atomeye.</code><code class="descname">set_delta</code><span class="sig-paren">(</span><em>delta</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#set_delta"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.set_delta" title="Permalink to this definition">¶</a></dt>
<dd><p>Set frame increment rate</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.first">
<code class="descclassname">atomeye.</code><code class="descname">first</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#first"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.first" title="Permalink to this definition">¶</a></dt>
<dd><p>Show the first frame (frame 0).</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.last">
<code class="descclassname">atomeye.</code><code class="descname">last</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#last"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.last" title="Permalink to this definition">¶</a></dt>
<dd><p>Show the last frame, i.e. len(gcv())-1</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.forward">
<code class="descclassname">atomeye.</code><code class="descname">forward</code><span class="sig-paren">(</span><em>delta=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#forward"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.forward" title="Permalink to this definition">¶</a></dt>
<dd><p>Move forward by <cite>delta</cite> frames (default value is gcv().delta).</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.backward">
<code class="descclassname">atomeye.</code><code class="descname">backward</code><span class="sig-paren">(</span><em>delta=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#backward"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.backward" title="Permalink to this definition">¶</a></dt>
<dd><p>Move backward by <cite>delta</cite> frames (default values is gcv().delta).</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.load_atom_color">
<code class="descclassname">atomeye.</code><code class="descname">load_atom_color</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#load_atom_color"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.load_atom_color" title="Permalink to this definition">¶</a></dt>
<dd><p>Load atom colours from a .clr file.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.load_aux">
<code class="descclassname">atomeye.</code><code class="descname">load_aux</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#load_aux"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.load_aux" title="Permalink to this definition">¶</a></dt>
<dd><p>Load aux property values from a .aux file.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.look_at_the_anchor">
<code class="descclassname">atomeye.</code><code class="descname">look_at_the_anchor</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#look_at_the_anchor"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.look_at_the_anchor" title="Permalink to this definition">¶</a></dt>
<dd><p>Equivalent to pressing the <cite>a</cite> key</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.observer_goto">
<code class="descclassname">atomeye.</code><code class="descname">observer_goto</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#observer_goto"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.observer_goto" title="Permalink to this definition">¶</a></dt>
<dd><p>Prompt for fractional position and move the observer there</p>
<p>Equivalent to pressing the <cite>g</cite> key.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.xtal_origin_goto">
<code class="descclassname">atomeye.</code><code class="descname">xtal_origin_goto</code><span class="sig-paren">(</span><em>s</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#xtal_origin_goto"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.xtal_origin_goto" title="Permalink to this definition">¶</a></dt>
<dd><p>Move the crystal origin to fractional coordinates <cite>s</cite></p>
<p>For example, use <code class="docutils literal notranslate"><span class="pre">s=[0.5,</span> <span class="pre">0.5,</span> <span class="pre">0.5]</span></code> to shift by half the cell along
the <span class="math notranslate nohighlight">\(\mathbf{a}\)</span>, <span class="math notranslate nohighlight">\(\mathbf{b}\)</span> and <span class="math notranslate nohighlight">\(\mathbf{c}\)</span>
lattice vectors.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.find_atom">
<code class="descclassname">atomeye.</code><code class="descname">find_atom</code><span class="sig-paren">(</span><em>i</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#find_atom"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.find_atom" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the anchor to the atom with index <cite>i</cite>.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.resize">
<code class="descclassname">atomeye.</code><code class="descname">resize</code><span class="sig-paren">(</span><em>width</em>, <em>height</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#resize"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.resize" title="Permalink to this definition">¶</a></dt>
<dd><p>Resize the current window to <cite>width</cite> x <cite>height</cite> pixels.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.change_aux_colormap">
<code class="descclassname">atomeye.</code><code class="descname">change_aux_colormap</code><span class="sig-paren">(</span><em>n</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#change_aux_colormap"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.change_aux_colormap" title="Permalink to this definition">¶</a></dt>
<dd><p>Select the <cite>n</cite>-th auxiliary property colourmap.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.draw_arrows">
<code class="descclassname">atomeye.</code><code class="descname">draw_arrows</code><span class="sig-paren">(</span><em>property</em>, <em>scale_factor=0.0</em>, <em>head_height=0.1</em>, <em>head_width=0.05</em>, <em>up=(0.0</em>, <em>1.0</em>, <em>0.0)</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#draw_arrows"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.draw_arrows" title="Permalink to this definition">¶</a></dt>
<dd><p>Draw arrows on each atom, based on a vector property</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><dl class="first last docutils">
<dt><strong>property</strong> <span class="classifier-delimiter">:</span> <span class="classifier">string</span></dt>
<dd><p class="first last">Name of the array to use for arrow vectors.
Use <code class="docutils literal notranslate"><span class="pre">None</span></code> to turn off previous arrows.</p>
</dd>
<dt><strong>scale_factor</strong> <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
<dd><p class="first last">Override length of arrows. 1 unit = 1 Angstrom; default
value of 0.0 means autoscale.</p>
</dd>
<dt><strong>head_height</strong> <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
<dd><p class="first last">Specify height of arrow heads in Angstrom.</p>
</dd>
<dt><strong>head_width</strong> <span class="classifier-delimiter">:</span> <span class="classifier">float</span></dt>
<dd></dd>
<dt><strong>up</strong> <span class="classifier-delimiter">:</span> <span class="classifier">3-vector (tuple, list or array)</span></dt>
<dd><p class="first last">Specify the plane in which the arrow heads are
drawn. Arrows are drawn in the plane which is common
to their direction and this vector.
Default is <code class="docutils literal notranslate"><span class="pre">[0.,1.,0.]</span></code>.</p>
</dd>
</dl>
</td>
</tr>
</tbody>
</table>
</dd></dl>

<dl class="function">
<dt id="atomeye.wait">
<code class="descclassname">atomeye.</code><code class="descname">wait</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#wait"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.wait" title="Permalink to this definition">¶</a></dt>
<dd><p>Sleep until current AtomEye viewer has finished processing all queued events.</p>
</dd></dl>

<dl class="function">
<dt id="atomeye.display">
<code class="descclassname">atomeye.</code><code class="descname">display</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/atomeye.html#display"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#atomeye.display" title="Permalink to this definition">¶</a></dt>
<dd><p>Display snapshot from current viewer in Jupyter notebook</p>
</dd></dl>

</div>


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